def createDocument(self, base_doc: DocT = None):
global CNMainWindow
# print("CadnanoQt createDocument begin")
default_file = self.argns.file or os.environ.get(
'CADNANO_DEFAULT_DOCUMENT', None)
if default_file is not None and base_doc is not None:
default_file = os.path.expanduser(default_file)
default_file = os.path.expandvars(default_file)
dw = CNMainWindow(base_doc)
self.cnmain_windows.add(dw)
# logger.info("Loading cadnano file %s to base document %s", default_file, base_doc)
decodeFile(default_file, document=base_doc)
dw.setFileName(default_file)
print("Loaded default document: %s" % (default_file))
else:
doc_window_count = len(self.cnmain_windows)
# logger.info("Creating new empty document...")
if doc_window_count == 0: # first dw
# dw adds itself to app.cnmain_windows
dw = CNMainWindow(base_doc)
self.cnmain_windows.add(dw)
elif doc_window_count == 1: # dw already exists
dw = list(self.cnmain_windows)[0]
dw.newDocument() # tell it to make a new doucment
# print("CadnanoQt createDocument done")
return dw.document()
def createDocument(self, base_doc: DocT = None):
global CNMainWindow
# print("CadnanoQt createDocument begin")
default_file = self.argns.file or os.environ.get('CADNANO_DEFAULT_DOCUMENT', None)
if default_file is not None and base_doc is not None:
default_file = os.path.expanduser(default_file)
default_file = os.path.expandvars(default_file)
dw = CNMainWindow(base_doc)
self.cnmain_windows.add(dw)
# logger.info("Loading cadnano file %s to base document %s", default_file, base_doc)
decodeFile(default_file, document=base_doc)
dw.setFileName(default_file)
print("Loaded default document: %s" % (default_file))
else:
doc_window_count = len(self.cnmain_windows)
# logger.info("Creating new empty document...")
if doc_window_count == 0: # first dw
# dw adds itself to app.cnmain_windows
dw = CNMainWindow(base_doc)
self.cnmain_windows.add(dw)
elif doc_window_count == 1: # dw already exists
dw = list(self.cnmain_windows)[0]
dw.newDocument() # tell it to make a new doucment
# print("CadnanoQt createDocument done")
return dw.document()
def testDisplay():
designname = "Nature09_monolith.json"
inputfile = pjoin(TEST_PATH,
"data", designname)
doc = cndecode.decodeFile(inputfile)
part = doc.activePart()
displayVHs(part, camera_z = 70)
def readFile(self, filename):
""" Convenience wrapper for `decodeFile` to always emit_signals and
set the `document` argument to `self`
Args:
filename (str): full path file name
"""
print("reading file", filename)
return decodeFile(filename, document=self, emit_signals=True)
def readFile(self, filename: str) -> DocT:
"""Convenience wrapper for ``decodeFile`` to always emit_signals and
set the ``document`` argument to ``self``
Args:
filename: full path file name
Returns:
self ``Document`` object with data decoded from ``filename``
"""
print("reading file", filename)
return decodeFile(filename, document=self, emit_signals=True)
def readFile(self, filename: str) -> DocT:
"""Convenience wrapper for ``decodeFile`` to always emit_signals and
set the ``document`` argument to ``self``
Args:
filename: full path file name
Returns:
self ``Document`` object with data decoded from ``filename``
"""
print("reading file", filename)
return decodeFile(filename, document=self, emit_signals=True)
def createDocument(self, base_doc: DocT = None):
global DocumentController
# print("CadnanoQt createDocument begin")
default_file = self.argns.file or os.environ.get('CADNANO_DEFAULT_DOCUMENT', None)
if default_file is not None and base_doc is not None:
default_file = os.path.expanduser(default_file)
default_file = os.path.expandvars(default_file)
dc = DocumentController(base_doc)
# logger.info("Loading cadnano file %s to base document %s", default_file, base_doc)
decodeFile(default_file, document=base_doc)
dc.setFileName(default_file)
print("Loaded default document: %s" % (default_file))
else:
doc_ctrlr_count = len(self.document_controllers)
# logger.info("Creating new empty document...")
if doc_ctrlr_count == 0: # first dc
# dc adds itself to app.document_controllers
dc = DocumentController(base_doc)
elif doc_ctrlr_count == 1: # dc already exists
dc = list(self.document_controllers)[0]
dc.newDocument() # tell it to make a new doucment
# print("CadnanoQt createDocument done")
return dc.document()
def loadFile(filename: str) -> DocT:
inputfile = pjoin(TEST_PATH,
"data", filename)
doc = cndecode.decodeFile(inputfile)
return doc
def loadFile(filename: str) -> DocT:
inputfile = pjoin(TEST_PATH, "data", filename)
doc = cndecode.decodeFile(inputfile)
return doc
def testDisplay():
designname = "Nature09_monolith.json"
inputfile = pjoin(TEST_PATH, "data", designname)
doc = cndecode.decodeFile(inputfile)
part = doc.activePart()
displayVHs(part, camera_z=70)
root_path = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
sys.path.append(root_path)
BASE_LENGTH = 0.3
if __name__ == "__main__":
test1 = 'super_barcode_hex.json'
test2 = 'Nature09_squarenut.json'
path_out = 'Nature09_squarenut.stl'
root_path = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
test_path = os.path.join(root_path, 'tests', test2)
doc = decode.decodeFile(test_path)
solids = []
part = doc.children()[0]
# print(part.radius())
radius = part.radius() + 0.1
for oligo in part.oligos():
if not oligo.isStaple():
strand5p = oligo.strand5p()
for strand in strand5p.generator3pStrand():
length = BASE_LENGTH*strand.length()
idx_low, idx_high = strand.idxs()
z = BASE_LENGTH*((idx_high + idx_low) / 2.0)
